BioC 3.0: CHECK report for KEGGgraph on oaxaca

Package: KEGGgraph

Version: 1.24.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.24.0.tar.gz

StartedAt: 2015-04-10 00:47:44 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 00:49:19 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 94.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: KEGGgraph.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch KEGGgraph_1.24.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/KEGGgraph.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘KEGGgraph/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘KEGGgraph’ version ‘1.24.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘KEGGgraph’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘methods’ ‘XML’ ‘graph’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘KEGG.db’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.subtypeDisplay: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGgraphLegend: no visible binding for global variable
  ‘KEGGEdgeSubtype’
KEGGpathway2Graph: no visible global function definition for
  ‘nodeDataDefaults<-’
KEGGpathway2Graph: no visible global function definition for
  ‘edgeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘ftM2graphNEL’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘nodeDataDefaults<-’
KEGGpathway2reactionGraph: no visible global function definition for
  ‘edgeDataDefaults<-’
getKEGGnodeData: no visible global function definition for ‘nodeData’
graphDensity: no visible global function definition for ‘numEdges’
graphDensity: no visible global function definition for ‘numNodes’
kgmlFileName2PathwayName: no visible binding for global variable
  ‘KEGGPATHID2NAME’
mergeKEGGgraphs : <anonymous>: no visible global function definition
  for ‘nodeDataDefaults’
mergeKEGGgraphs : <anonymous>: no visible global function definition
  for ‘edgeDataDefaults’
mergeKEGGgraphs: no visible global function definition for
  ‘nodeDataDefaults<-’
mergeKEGGgraphs: no visible global function definition for
  ‘edgeDataDefaults<-’
plotKEGGgraph: no visible global function definition for
  ‘edgeRenderInfo<-’
plotKEGGgraph: no visible global function definition for
  ‘nodeRenderInfo<-’
plotKEGGgraph: no visible global function definition for ‘layoutGraph’
plotKEGGgraph: no visible global function definition for ‘renderGraph’
randomSubGraph : <anonymous>: no visible global function definition for
  ‘subGraph’
setKEGGedgeData: no visible global function definition for
  ‘edgeDataDefaults<-’
setKEGGnodeData: no visible global function definition for
  ‘nodeDataDefaults<-’
subGraphByNodeType: no visible global function definition for
  ‘subGraph’
subKEGGgraph: no visible global function definition for ‘subGraph’
subKEGGgraph: no visible global function definition for
  ‘nodeDataDefaults’
subKEGGgraph: no visible global function definition for
  ‘edgeDataDefaults’
subKEGGgraph: no visible global function definition for
  ‘nodeDataDefaults<-’
subKEGGgraph: no visible global function definition for
  ‘edgeDataDefaults<-’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [25s/26s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘kegg2graph.R’ [12s/12s]
  Running ‘testGraph.R’ [2s/2s]
 [14s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

WARNING: There was 1 warning.
NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/KEGGgraph.Rcheck/00check.log’
for details.

* installing *source* package ‘KEGGgraph’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (KEGGgraph)

name	user	system	elapsed
KEGGEdge-class	0.692	0.005	0.701
KEGGEdgeSubType-class	0.001	0.000	0.002
KEGGEdgeSubtype	0.010	0.001	0.018
KEGGGraphics-class	0.002	0.000	0.001
KEGGGroup-class	0.002	0.001	0.001
KEGGNode-class	0.394	0.001	0.401
KEGGPathway-class	0.654	0.002	0.660
KEGGPathwayInfo-class	0.440	0.005	0.444
KEGGReaction-class	0.642	0.003	0.649
KEGGpathway2Graph	0.453	0.003	0.457
KEGGpathway2reactionGraph	0.736	0.003	0.740
expandKEGGPathway	0.926	0.007	0.935
getDisplayName-methods	0.383	0.002	0.387
getEntryID-methods	0.397	0.002	0.406
getKEGGID-methods	0.203	0.001	0.204
getKEGGgeneLink-methods	0.001	0.000	0.000
getKEGGnodeData	1.093	0.007	1.122
getKGMLurl	0.006	0.003	0.199
getName-methods	0.409	0.002	0.412
getNamedElement	0.001	0.000	0.001
getPathwayInfo-methods	0.418	0.002	0.420
getReactions-methods	0.700	0.003	0.716
getRgraphvizEdgeNames	0.002	0.000	0.003
getSubtype-methods	0.416	0.002	0.419
getTitle-methods	0.403	0.002	0.407
getType-methods	0.723	0.003	0.729
graphDensity	0.002	0.000	0.003
isHomoList	0.001	0.001	0.001
mergeKEGGgraphs	2.155	0.010	2.191
neighborhood	0.216	0.008	0.374
parseKGML	0.392	0.002	0.395
parseKGML2DataFrame	2.403	0.010	2.480
parseKGML2Graph	1.180	0.004	1.210
plotKEGGgraph	2.262	0.013	2.339
pvalue2asterisk	0.001	0.000	0.001
queryKEGGsubgraph	1.086	0.006	1.105
randomSubGraph	0.02	0.00	0.02
splitKEGGgroup	0.415	0.002	0.419
subGraphByNodeType	0.991	0.006	1.003
subKEGGgraph	1.062	0.005	1.079
translateKEGGID2GeneID	0.001	0.000	0.001
translateKEGGgraph	1.185	0.004	1.197